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Detailed information for vg0707257565:

Variant ID: vg0707257565 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7257565
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGTACCCCTCCTCCCGCGGCAAGGAGCTCTGGGTGAAAACCTAGTCCAGTTTTTTGGACGGATGATGACGGCGTCTTTCGGCGTTACGACCCTCGTGA[A/G]
GGCGTCGTTTTTGAGTCTTCGTGTCATGGTGGTGTTGTTGGCCCGGTGGCGATCGGTCTAGCATAGTGATGGTCGGTTCGATGCTTAGCTTCTCTCTCTG

Reverse complement sequence

CAGAGAGAGAAGCTAAGCATCGAACCGACCATCACTATGCTAGACCGATCGCCACCGGGCCAACAACACCACCATGACACGAAGACTCAAAAACGACGCC[T/C]
TCACGAGGGTCGTAACGCCGAAAGACGCCGTCATCATCCGTCCAAAAAACTGGACTAGGTTTTCACCCAGAGCTCCTTGCCGCGGGAGGAGGGGTACCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.30%	15.90%	4.82%	57.02%	NA
All Indica	2759	1.50%	4.10%	5.26%	89.09%	NA
All Japonica	1512	49.90%	41.10%	4.03%	4.89%	NA
Aus	269	56.90%	0.40%	4.83%	37.92%	NA
Indica I	595	0.20%	1.20%	5.38%	93.28%	NA
Indica II	465	2.20%	5.80%	7.74%	84.30%	NA
Indica III	913	1.10%	0.90%	3.18%	94.85%	NA
Indica Intermediate	786	2.70%	9.20%	6.11%	82.06%	NA
Temperate Japonica	767	23.90%	69.40%	5.87%	0.91%	NA
Tropical Japonica	504	72.00%	14.30%	1.79%	11.90%	NA
Japonica Intermediate	241	86.70%	7.50%	2.90%	2.90%	NA
VI/Aromatic	96	77.10%	0.00%	0.00%	22.92%	NA
Intermediate	90	31.10%	15.60%	10.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707257565	A -> DEL	N	N	silent_mutation	Average:15.585; most accessible tissue: Callus, score: 78.162	N	N	N	N
vg0707257565	A -> G	LOC_Os07g12690.1	upstream_gene_variant ; 4937.0bp to feature; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Callus, score: 78.162	N	N	N	N
vg0707257565	A -> G	LOC_Os07g12700.1	downstream_gene_variant ; 490.0bp to feature; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Callus, score: 78.162	N	N	N	N
vg0707257565	A -> G	LOC_Os07g12710.1	downstream_gene_variant ; 1049.0bp to feature; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Callus, score: 78.162	N	N	N	N
vg0707257565	A -> G	LOC_Os07g12700-LOC_Os07g12710	intergenic_region ; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Callus, score: 78.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707257565	NA	5.49E-06	mr1057	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0707257565	4.31E-06	4.31E-06	mr1261	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0707257565	NA	1.00E-12	mr1657	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0707257565	NA	1.32E-08	mr1827	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0707257565	NA	1.29E-06	mr1064_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0707257565	NA	3.00E-06	mr1341_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251